inprogress

[jalview.git] / forester / java / src / org / forester / surfacing / CombinableDomains.java

diff --git a/forester/java/src/org/forester/surfacing/CombinableDomains.java b/forester/java/src/org/forester/surfacing/CombinableDomains.java
index 05fffbf..28fa0e2 100644 (file)
--- a/forester/java/src/org/forester/surfacing/CombinableDomains.java
+++ b/forester/java/src/org/forester/surfacing/CombinableDomains.java
@@ -6,7 +6,7 @@
 // Copyright (C) 2008-2009 Christian M. Zmasek
 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
 // All rights reserved
-// 
+//
 // This library is free software; you can redistribute it and/or
 // modify it under the terms of the GNU Lesser General Public
 // License as published by the Free Software Foundation; either
@@ -16,20 +16,22 @@
 // but WITHOUT ANY WARRANTY; without even the implied warranty of
 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 // Lesser General Public License for more details.
-// 
+//
 // You should have received a copy of the GNU Lesser General Public
 // License along with this library; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
 import java.util.List;
+import java.util.Set;
 import java.util.SortedMap;
 
-import org.forester.util.DescriptiveStatistics;
+import org.forester.protein.BinaryDomainCombination;
+import org.forester.species.Species;
 
 public interface CombinableDomains {
 
@@ -38,18 +40,7 @@ public interface CombinableDomains {
      * 
      * @param protein_domain
      */
-    public void addCombinableDomain( final DomainId protein_domain );
-
-    /**
-     * 
-     * This must return all domains in this set of combinable domains (i.e.
-     * the key domain and all domains which can combine with the key domain).
-     * 
-     *  @return all domains
-     */
-    List<DomainId> getAllDomains();
-
-    List<DomainId> getCombinableDomains();
+    public void addCombinableDomain( final String protein_domain );
 
     /**
      * Returns the combinable domain identifiers sorted in alphabetical manner: -
@@ -58,7 +49,7 @@ public interface CombinableDomains {
      * 
      * @return combining domain identifiers sorted in alphabetical manner
      */
-    public SortedMap<DomainId, Integer> getCombinableDomainsIds();
+    public SortedMap<String, Integer> getCombinableDomainsIds();
 
     public StringBuilder getCombiningDomainIdsAsStringBuilder();
 
@@ -68,16 +59,7 @@ public interface CombinableDomains {
      * 
      * @return the domain identifier
      */
-    public DomainId getKeyDomain();
-
-    /**
-     * Gets descriptive statistics for the confidence (i.e. E-values) of the key
-     * domain.
-     * 
-     * 
-     * @return descriptive statistics for the confidence of the key domain
-     */
-    public DescriptiveStatistics getKeyDomainConfidenceDescriptiveStatistics();
+    public String getKeyDomain();
 
     /**
      * Returns how many times the key domain is present in a given species
@@ -87,6 +69,8 @@ public interface CombinableDomains {
      */
     public int getKeyDomainCount();
 
+    public Set<String> getKeyDomainProteins();
+
     /**
      * Returns how many proteins with the key domain are present in a given
      * species genome.
@@ -97,7 +81,7 @@ public interface CombinableDomains {
 
     public int getNumberOfCombinableDomains();
 
-    public int getNumberOfProteinsExhibitingCombination( final DomainId protein_domain );
+    public int getNumberOfProteinsExhibitingCombination( final String protein_domain );
 
     /**
      * Returns the species of this combinable domains.
@@ -106,16 +90,22 @@ public interface CombinableDomains {
      */
     public Species getSpecies();
 
-    public boolean isCombinable( final DomainId protein_domain );
+    public boolean isCombinable( final String protein_domain );
+
+    public List<BinaryDomainCombination> toBinaryDomainCombinations();
+
+    void addKeyDomainProtein( String protein );
 
     /**
-     * This is to set descriptive statistics for the confidence (i.e. E-values)
-     * of the key domain.
      * 
+     * This must return all domains in this set of combinable domains (i.e.
+     * the key domain and all domains which can combine with the key domain).
      * 
-     * @param statistics
+     *  @return all domains
      */
-    void setKeyDomainConfidenceDescriptiveStatistics( final DescriptiveStatistics statistics );
+    List<String> getAllDomains();
+
+    List<String> getCombinableDomains();
 
     /**
      * Sets how many times the key domain is present in a given species genome.
@@ -124,15 +114,4 @@ public interface CombinableDomains {
      *            key domain count in species
      */
     void setKeyDomainCount( final int key_domain_count );
-
-    /**
-     * Sets how many proteins with the key domain are present in a given species
-     * genome.
-     * 
-     * @param key_domain_proteins_count
-     *            key domain protein count in species
-     */
-    void setKeyDomainProteinsCount( final int key_domain_proteins_count );
-
-    public List<BinaryDomainCombination> toBinaryDomainCombinations();
 }
\ No newline at end of file